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comparison mutational_patterns.xml @ 1:921c1f55481d draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit ca3b3ab85c8224821c76ebd56b1be2441a28f609"
author artbio
date Sun, 13 Sep 2020 22:27:03 +0000
parents 924c527fb379
children aea952be68cb
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0:924c527fb379 1:921c1f55481d
1 <tool id="mutational_patterns" name="Analyse Mutational Patters/Signatures" version="2.0.0_galaxy_1"> 1 <tool id="mutational_patterns" name="Analyse Mutational Patters/Signatures" version="2.0.0_galaxy_2">
2 <description>from genomic variations in vcf files</description> 2 <description>from genomic variations in vcf files</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.0.0=r40_0">bioconductor-mutationalpatterns</requirement> 4 <requirement type="package" version="2.0.0=r40_0">bioconductor-mutationalpatterns</requirement>
5 <requirement type="package" version="1.6.6=r40h6115d3f_1">r-optparse</requirement> 5 <requirement type="package" version="1.6.6=r40h6115d3f_1">r-optparse</requirement>
6 <requirement type="package" version="0.2.20=r40h0357c0b_1002">r-rjson</requirement> 6 <requirement type="package" version="0.2.20=r40h0357c0b_1002">r-rjson</requirement>
88 * the number of cosmic signatures to decompose mutational patterns of samples 88 * the number of cosmic signatures to decompose mutational patterns of samples
89 89
90 90
91 This tool returns a pdf file with the visualisation : 91 This tool returns a pdf file with the visualisation :
92 92
93 * the Cosine similarity of samples when decomposed over the 30 signatures of cosmic 93 * the Cosine similarity of samples when decomposed over the 30 signatures of cosmic_
94 * the absolute contribution of the n most contributing cosmic signatures in the samples mutational patterns (to be set by the user, between 2 and 30) 94 * the absolute contribution of the n most contributing cosmic_ signatures in the samples mutational patterns (to be set by the user, between 2 and 30)
95 * the relative contribution of the n most contributing cosmic signatures in the samples mutational patterns (to be set by the user, between 2 and 30) 95 * the relative contribution of the n most contributing cosmic_ signatures in the samples mutational patterns (to be set by the user, between 2 and 30)
96 * a clustering of the samples with respect to the relative contribution of their cosmic signatures 96 * a clustering of the samples with respect to the relative contribution of their cosmic_ signatures
97 * pie charts of the samples displaying for each sample the relative contribution of the n most contributing cosmic signatures in their mutational pattern 97 * pie charts of the samples displaying for each sample the relative contribution of the n most contributing cosmic_ signatures in their mutational pattern
98 98
99 .. _cosmic: https://cancer.sanger.ac.uk/cosmic/signatures_v2.tt
99 100
100 </help> 101 </help>
101 <citations> 102 <citations>
102 <citation type="doi">10.18129/B9.bioc.MutationalPatterns</citation> 103 <citation type="doi">10.18129/B9.bioc.MutationalPatterns</citation>
103 <citation type="doi">10.1186/s13073-018-0539-0</citation> 104 <citation type="doi">10.1186/s13073-018-0539-0</citation>